Dirk van der Marel

working with the Scanning Electron Microscope (SEM)

My work at the laboratory focuses mainly on Geology but I also assist research in the biological sector. I am experienced in assisting the Netherlands Gemmological Laboratory, including UVVIS, FTIR, XRF (micro-spot X-ray analysis and mapping), 3D and 2D Xray imaging and many more techniques. The Gemmological Laboratory is part of Naturalis. My latest expertise is operating the XRADIA Versa 520 micro-CT scanner for a broad-based internal and external support. 


Light Microscope, SEM, FEG SEM, Xradia Versa 520, Skyscan, FTIR, UVVIS, Faxitron, Raman, Edax XRF, NEL

Dirk van der Marel

Research technician
Netherlands Gemmological Laboratory

+31 (0)71 751 9665



My favorite objects for 3D X-ray imaging are fossils, pearls, insects and NFI materials.

While working at The Netherlands Gemmological Laboratory my favorite research instruments are the Orbis X-Ray element detection and element mapping, FTIR (Infrared spectroscopy) and UVVIS (Ultraviolet–visible spectroscopy).

My favorite stone is the natural sapphire from Kashmir. Sapphires were first discovered in Kashmir around 1880. The most marked feature is a distinct growth zoning, which usually results in a pattern of alternating transparent and slightly “milky” growth bands.

One of my goals is providing technical assistance within the Netherlands Gemmological Laboratory by testing pearls, cut and rough minerals. I use a variety of instruments such as the UVVIS, FTIR, 2D and 3D X-Ray technics. Element testing on the Orbis Micro-XRF Analyzer, that incorporate fast, simultaneous multi-element X-ray detection with the sensitivity to analyze from parts-per-million to 100% concentrations. Technics that will help to identify minerals (cut or rough).

Another goal is providing technical assistance for most research departments to analyse material within the Naturalis collection such as bone, plants and insects etc. by using 3D-X-ray imaging technics with a minimal spatial resolution of 0.7 μm resolution.

3D Toed

a dragonfly


At the laboratories of Naturalis Biodiversity Center


An unknown dragonfly species has been observed around Naturalis, which is being caught. After this it will start a journey through the different labs. He is viewed / analyzed with various devices. The people who work with this in daily practice explain this. In the end, everything appears to indicate that it is an exotic dragonfly that a researcher at Naturalis Biodiversity Center has described.

A day at the lab

about the different research techniques

  • SEM (JSM-6480 LV)

SEM LVThe Jeol JSM-6480 LV is a high-performance, scanning electron microscope with a high resolution of 3.0nm. The low vacuum mode (which can be accessed by the click of a mouse), allows for observation of specimens which cannot be viewed at high vacuum due to excessive water content or due to a non-conductive surface. Its asynchronous five-axis eucentric stage with compucentric rotation and tilt can accommodate a specimen of up to 8-inches in diameter. Standard automated features include Auto Focus/Auto Stigmator, Auto Gun (saturation and alignment), and Automatic Contrast and Brightness.


  • FEG SEM (JSM-7600)

FegsemThe JSM-7600 FEG SEM is a Field Emission Scanning Electron Microscope suitable to study surface structures at magnifications from 25x to 1.000.000x. A Scanning Microscope (SEM) sends a fine electron beam onto the sample. This generates secondary electrons which reflect from the surface of the sample. These secondary electrons are detected by the SEM and used to form an image showing the surface of the specimen. A Field Emisson Gun (FEG) generates a very fine beam that is suitable to give a very high resolution image.


  • Xradia Versa 520  (3D Micro X-Ray imaging)

Zeiss XradiaZEISS Xradia 520 Versa 3D X-ray microscope opens up new degrees of flexibility for scientific discovery and builds on industry-best resolution and contrast, and expands the boundaries of non-destructive imaging for breakthrough flexibility and discernment critical for research. The Xradia 520 Versa achieves minimum achievable voxel of 70 nm and spatial resolution of 0.7 µm.




  • Skyscan 1172  (3D Micro X-Ray imaging)

SkyscanBriefly, the system obtains multiple x-ray “shadow” transmission images of the object from multiple angular views as the object rotates on a high-precision stage. From these shadow images, cross-section images of the object are reconstructed using a modified Feldkamp cone-beam algorithm, creating a complete 3D representation of internal microstructure and density over an investigator-selected horizontal region in the transmission images.

The Skyscan 1172, 50mm FOV (image field width) is a desktop ex vivo microCT specimen scanner. This instrument has a fully distortioncorrected 11Mp X-ray camera that is a 12-bit cooled CCD fiber-optically camera coupled to scintillator. The X-ray source is 20-100kV, 10W, with a <5µm spot size. The detail detectability is 1µm at highest resolution to 25µm. Importantly, the Skyscan 1172 has an innovative dynamically variable acquisition geometry that provides the shortest scan times possible at any magnification (adaptive geometry features explained more fully below). Cross-section images are generated in a wide range of formats up to 8000 x 8000 pixels. The maximum object size is 50mm in diameter or height. Reconstruction can be performed using either a single PC or using the cluster of 4-PCs in the core facility to enhance post-scan reconstruction times.


  • FTIR (Nicolet iS50 FTIR Spectrometer)

FTIRFourier-transform infrared spectroscopy (FTIR) is a technique used to obtain an infrared spectrum of absorption or emission of a solid, liquid or gas. An FTIR spectrometer simultaneously collects high-spectral-resolution data over a wide spectral range. FTIR is an analytical technique used to identify organic, polymeric, and, in some cases, inorganic materials. The FTIR analysis method uses infrared light to scan test samples and observe chemical properties. 

The Nicolet iS50 Spectrometer performs chemical analyses of sample materials by colleting data in the Mid-IR, far-IR and near-IR spectral ranges using a variety of accessories. The system integrates advanced instrument features, such as step-scan and dual-channel data collection, with a matching software suite and many other features that make data collection easy. This system has a variety of upgrade options including built-in ATR, an automated beamsplitter exchanger and Raman, NIR, TGA-IR and GC-IR modules.


  • UVVIS (Thermo Scientific Evolution 600)

UVVISUltraviolet-visible spectroscopy is considered an important tool in analytical chemistry. In fact, this is one of the most commonly used techniques in clinical as well as chemical laboratories. This tool is used for the qualitative analysis and identification of chemicals. However, its main use is for the quantitative determination of different organic and inorganic compounds in solution. Basically, spectroscopy is related to the interaction of light with matter. As light is absorbed by matter, the result is an increase in the energy content of the atoms or molecules. The absorption of visible light or ultraviolet light by a chemical compound will produce a distinct spectrum. When ultraviolet radiations are absorbed, this results in the excitation of the electrons from the ground state towards a higher energy state. The theory revolving around this concept states that the energy from the absorbed ultraviolet radiation is actually equal to the energy difference between the higher energy state and the ground state.

The Thermo Scientific Evolution 600 is a dual beam scanning UV-vis spectrophotometer for routine use. It has a wavelength range from 190-900 nm and is equipped with variable slits for high resolution or high sensitivity absorbance measurements. The instrument has built in control modules for kinetics and quantative analysis. The instrument is located in conjunction with a pair of potentiostats for spectroelectrochemical measurements. 


  • Faxitron  (2D X-Ray imaging Cabinet System 43855)

FaxitronThe Faxitron Cabinet X-ray System 43855 is a self-contained, radiation-shielded cabinet X-ray system designed to give high resolution radiographs of small to medium-size objects of all types. Simple operating techniques and radiation safety features made the Faxitron usually convenient in scientific and industrial X-ray inspection, quality control, reliability, and failure analysis or other operations requiring nondestructive testing techniques. High resolution by means of the microfocus options, also makes it very useful for medical pathology.





  • Raman (Thermo Scientific DXR)


The DXR Raman microscope is a research-quality tool designed specifically for today’s multi-purpose analytical labs. This is the microscope for the user who needs the high spatial resolution, ease of sample preparation and power of Raman microscopy, and who has neither the time nor the desire to become a Raman expert. The DXR Raman microscope delivers spatial resolution that is as good or better than any instrument on the market, together with unique features designed to make it as easy as possible to get high quality results. Users can configure the DXR Raman microscope with up to three different excitation wavelengths – at 532, 633 and 780 nm. The lasers, together with the appropriate filters and gratings, lock into place using SmartLock technology for precisely reproducible results. OMNIC™ software recognizes each component, records the serial numbers and checks for compatibility. A convenient storage container is provided for when the components are not in use.


  •  XRF - Edax (Orbis Micro-XRF Analyzer)

EdaxXRF is the emission of characteristic "secondary" (or fluorescent) X-rays from a material that has been excited by bombarding with high-energy X-rays or gamma rays. The phenomenon is widely used for elemental analysis and chemical analysis, particularly in the investigation of metals, glass, ceramics and building materials, and for research in mineralogy (rough and cut gemstones), petrology, forensic science, archaeology and many more. All elements from atomic number 4 (Be) to 92 (U) can be detected in principle, though not all instruments are equipped for 'light' elements (Z < 10). Qualitative analysis involves the identification of the lines in the spectrum and is fairly straightforward owing to the simplicity of X-ray spectra. Quantitative analysis (determination of the concentrations of the elements present) entails measuring line intensities for each element in the sample and for the same elements in calibration Standards of known composition.



The Coiled Genitalia of a Mosquito
made with the Xradia Versa 520 (3D Micro X-Ray imaging)

3D genitalia of a mosquito


  • Assisting researchers and teaching students with operating the Scanning Electron Microscope (SEM) and 3D imaging X-ray machines.
  • Teaching students with operating the Edax XRF (micro-spot X-ray analysis and mapping), 2D X-Ray imaging and other laboratory techniques


  • Zwaan J.C., Marel D. van der, Dommisse H.A. 2014. The ‘Sleeping Lion’ Baroque Pearl: An Update. Journal of Gemmology 34: 248-253. Go to website